5OMV

Ternary complex of 9N DNA polymerase in the replicative state with two metal ions in the active site

• PDB DOI: https://doi.org/10.2210/pdb5OMV/pdb
• NAKB: 5OMV

• Classification: TRANSFERASE
• Organism(s): Thermococcus sp. 9oN-7, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2017-08-01 Released: 2017-12-20 
• Deposition Author(s): Betz, K., Marx, A., Diederichs, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 

Starting Model: experimental

Literature

Crystal structures of ternary complexes of archaeal B-family DNA polymerases.

Kropp, H.M., Betz, K., Wirth, J., Diederichs, K., Marx, A.

(2017) PLoS One 12: e0188005-e0188005

• PubMed: 29211756 
• DOI: https://doi.org/10.1371/journal.pone.0188005
• Primary Citation of Related Structures:  
  5OMF, 5OMQ, 5OMV


• PubMed Abstract: 
  

  Archaeal B-family polymerases drive biotechnology by accepting a wide substrate range of chemically modified nucleotides. By now no structural data for archaeal B-family DNA polymerases in a closed, ternary complex are available, which would be the basis for developing next generation nucleotides. We present the ternary crystal structures of KOD and 9°N DNA polymerases complexed with DNA and the incoming dATP. The structures reveal a third metal ion in the active site, which was so far only observed for the eukaryotic B-family DNA polymerase δ and no other B-family DNA polymerase. The structures reveal a wide inner channel and numerous interactions with the template strand that provide space for modifications within the enzyme and may account for the high processivity, respectively. The crystal structures provide insights into the superiority over other DNA polymerases concerning the acceptance of modified nucleotides.

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Organizational Affiliation: 

Konstanz Research School Chemical Biology, University of Konstanz, Baden-Württemberg, Konstanz, Germany.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 99.36 kDa 
• Atom Count: 7,007 
• Modelled Residue Count: 785 
• Deposited Residue Count: 803 
• Unique protein chains: 1
• Unique nucleic acid chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
DNA polymerase	A	775	Thermococcus sp. 9oN-7	Mutation(s): 2  Gene Names: pol, polA EC: 2.7.7.7
UniProt
Find proteins for Q56366 (Thermococcus sp. (strain 9oN-7)) Explore Q56366  Go to UniProtKB:  Q56366

Entity ID: 2
Molecule	Chains	Length	Organism	Image
DNA template	B [auth T]	16	synthetic construct

Entity ID: 3
Molecule	Chains	Length	Organism	Image
DNA primer	C [auth P]	12	synthetic construct

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DTP (Subject of Investigation/LOI)	I [auth A]	2'-DEOXYADENOSINE 5'-TRIPHOSPHATE C10 H16 N5 O12 P3 SUYVUBYJARFZHO-RRKCRQDMSA-N
PGE	G [auth A], H [auth A]	TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N
GOL	E [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
MN	D [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
MG	F [auth A], J [auth T]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 0.233 
• R-Value Work: 0.189 
• R-Value Observed: 0.192 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.688	α = 90
b = 94.964	β = 90
c = 158.735	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-12-20 
Deposition Author(s): Betz, K., Marx, A., Diederichs, K.

Revision History  

• Version 1.0: 2017-12-20
  Type: Initial release
  
• Version 1.1: 2018-09-12
  Changes: Data collection, Database references
• Version 1.2: 2024-01-17
  Changes: Data collection, Database references, Derived calculations, Refinement description